Organic materials, with low environmental impact and adaptable structures, are attractive for Hybrid capacitive deionization (HCDI). However, the scarcity of active sites and tendency to dissolve in water-based solutions remain significant challenges. Herein, we synthesized a polynaphthalenequinoneimine (PCON) polymer with stable long-range ordered framework and rough three-dimensional floral surface morphology, along with high-density active sites provided by C=O and C=N functional groups, enabling efficient redox reactions and achieving a high Na+ capture capability. The synthesized PCON polymer showcases outstanding electroadsorption characteristics and notable structural robustness, attaining an impressive specific capacitance of 500.45 F g-1 at 1 A g-1 and maintaining 86.1% of its original capacitance following 5000 charge-discharge cycles. Benefiting from the superior pseudocapacitive properties of the PCON polymer, we developed an HCDI system that not only exhibits exceptional salt removal capacity of 100.8 mg g-1 and a remarkable rapid average removal rate of 3.36 mg g-1 min−1, but also maintains 97% of its initial desalination capacity after 50 cycles, thereby distinguishing itself with the comprehensive performance that significantly surpasses reported organic deionization materials. Prospectively, the synthesis paradigm of the double active-sites polymer may be extrapolated to other organic electrodes, heralding new avenues for the design of high-performance desalination systems.